Some people have reported problems with the filenames
in the distributes zip archive. Sometimes the
filenames get converted to lowercase when unpackig and
prepend.php can't find the required() files. Check prepend.php.

Only the first line of a doc comment gets used.

open

Yes, the parser uses the wrong linebreak sign. parser/PhpdocParserRegExp.php->$PHP_BASE["break"]
must be set to the userdefined constant LINEBREAK.

It can't handle OO code and procedural code in one file.

open

... will be solved until 1.0. See my hints on the
installation page
on how to work around.

The generated HTML documentation contains "1" but nothing else

open

This is not a really a bug. You have probably set a
template path with setTemplateRoot() that does not exists.

PHPDoc detects this but does not print the message public :|.
Some debugging/warning container must be introduced in the script.